Three-dimensional structural information is fundamental to elucidating the chemical and biological properties of molecules. The chemical reactivity and biological activity of a molecule are determined by both its two-dimensional (2-D) structure and three-dimensional (3-D) structure. For example, spatial complementarity is one major determinant of affinity of a ligand for a target compound. Tools to analyze and compare 3-D structures of molecules are critical to the advancement of structure-based ligand design efforts.
Experimental determination of the structures of all molecules under investigation as potential ligands for macromolecules is not realistic. Computational techniques to generate and manipulate 3-D structural representations of molecules have been developed. These techniques are based on experimental or computed geometries and/or rules about the construction of molecular models (reviewed in Sadowski and Gasteiger, Chem. Rev. 93:2567-2581, 1993).